Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.16.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97005	0.779
27DAP/17DAP	1.09402	0.89
39DAP/27DAP	1.08841	0.974
41DAP/39DAP	1.19566	0.328
42DAP/41DAP	1.09819	0.871
43DAP/42DAP	1.03722	1
47DAP/43DAP	1.00181	0.966
52DAP/47DAP	0.95379	0.842
57DAP/52DAP	1.0792	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16106	0.116
17DAP/reference	1.05111	0.33
27DAP/reference	1.03163	0.831
39DAP/reference	1.08369	0.294
41DAP/reference	1.17022	0.043
42DAP/reference	1.17553	0.004
43DAP/reference	0.99626	0.882
47DAP/reference	1.07929	0.042
52DAP/reference	1.19643	0.022
57DAP/reference	0.94083	0.096

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98155	0.75
27DAP/17DAP	0.98587	0.887
39DAP/27DAP	0.96745	0.628
41DAP/39DAP	1.04475	0.781
42DAP/41DAP	1.03247	0.727
43DAP/42DAP	1.00789	0.788
47DAP/43DAP	1.00979	0.95
52DAP/47DAP	0.9571	0.753
57DAP/52DAP	0.95084	0.39
57DAP/7DAP	0.9543	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07943	0.589
17DAP/reference	0.92653	0.124
27DAP/reference	0.86276
39DAP/reference	0.91519	0.011
41DAP/reference	0.88694	0.02
42DAP/reference	0.95476	0.037
43DAP/reference	0.99365	0.694
47DAP/reference	1.00902	1
52DAP/reference	1.00004	1
57DAP/reference	1.00528	1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0811	0.284
17DAP/reference	1.23933	0.009
27DAP/reference	1.20106	0.104
39DAP/reference	1.0716	0.377
41DAP/reference	1.02221	1
42DAP/reference	1.08624	0.24
43DAP/reference	1.10107	0.453
47DAP/reference	1.04239	0.291
52DAP/reference	1.10217	0.014
57DAP/reference	1.12402	0.07

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0994
17DAP/reference	1.02763	0.746
27DAP/reference	1.02188	0.644
39DAP/reference	0.95908	0.271
41DAP/reference	0.98436	0.237
42DAP/reference	0.98295	0.671
43DAP/reference	0.98024	0.66
47DAP/reference	0.95087	0.396
52DAP/reference	0.97774	0.781
57DAP/reference	0.88456	0.069

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95851	1
26DAP/20DAP	1.04506	0.839
34DAP/26DAP	0.91201	0.479
51DAP/34DAP	0.98637	0.901
52DAP/51DAP	0.99538	1
53DAP/52DAP	1.05129	0.688
55DAP/53DAP	0.98819	0.864
57DAP/55DAP	0.89727	0.452
62DAP/57DAP	0.93378	0.871
68DAP/62DAP	0.83523	0.505
68DAP/14DAP	0.6488	0.375

Experiment: Tomato (breaker-stage) vs. Pepper (breaker-stage)

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.16805	0.023

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.38995	0.058
Mature Green Tomato/Ripe Tomato	0.99723	0.835
Immature Eggplant/Mature Eggplant	1.27206	0.061
Ripe Pepper/Ripe Tomato	0.66901	0.224
Mature Eggplant/Ripe Tomato	0.85	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.04683
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	1.012	1
4-1-1/M82	N/A	N/A
4-1/M82	1.17809
4-3-2/M82	1.09648	1
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.88665
7-2/M82	N/A	N/A
9-3-2/M82	1.30652

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

Experiment: Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

hybridization	ratio	FDR (corrected p value)
10 h post inoculation	0.91865	0.497

Experiment: Time course of DC3000 vs delta hrp on tomato Prf-3

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.90199	1
DC3000/delta hrp 6h	1.16437	1
DC3000/delta hrp 12h	1.1848	1
DC3000/delta hrp 24h	0.86273	0.202

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.88393	0.196
DC3000 delta B/DC3000 delta AB	0.90198	0.1

Experiment: Matt's wild cherry tomato vs. Phytophthora infestans

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02686	1
Exp 36h	0.85954	0.449
Exp 60h	0.99952	1

Experiment: Gene expression profiling of infection of tomato by Phytophthora infestans in the field

hybridization	ratio	FDR (corrected p value)
self-self	0.99597	1
Var 0h	1.2653	0.936
Var 12h I row2-row1	0.97424	0.948
Var 12h NI row2-row1	0.90293	0.488
Var 36h I row2-row1	0.76407	0.805
Var 36h NI row2-row1	0.9322	0.61
Var 60h I row2-row1	1.33606	0.562
Var 60h NI row2-row1	1.01323	1
Time course 0hI-0hNI	1.0061	1
Time course 12hI-12hNI	0.99148	0.991
Time course 36hI-36hNI	0.87502	0.043
Time course 60hI-60hNI	0.68989	0.006

Experiment: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

hybridization	ratio	FDR (corrected p value)
transgenic ySAMdc/azygous control (mature green)	1.09198	0.297
transgenic ySAMdc/azygous control (breaker)	0.79484	0.137
transgenic ySAMdc/azygous control (red)	0.88685	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9728	0.242

Experiment: Microarray Analysis on Salt Stress Affected Genes in Tomato Seedlings

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.04449	1

Experiment: Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.99577	1
Manapal/WT (break)	0.78963	0.299
Manapal/WT (red)	0.93961	0.863